Jack Harrison played the corner short to Andrea Pirlo in the 52nd minute. Villa blocked Pirlo’s cross toward the goal line and followed it for a narrow-angle finish through the legs of Houston goalkeeper Joe Willis.
Villa nearly added a second in the 58th minute with a bending shot off the post. He completed the task in the 91st with a rising blast from the top of the box that moved him ahead of Bradley Wright-Phillips in the MLS Golden Boot race.
City (14-9-9) moved two points ahead of Toronto FC in the Eastern Conference standings. Houston (7-12-11) remained last in the West.
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